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- PDB-6f9z: Lysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f9z | ||||||
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Title | Lysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding. Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.3 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6f1lC ![]() 6f1mC ![]() 6f1oC ![]() 6f1pC ![]() 6f1rC ![]() 6f9xC ![]() 6f9yC ![]() 6fa0C ![]() 4e3uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14060.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % / Mosaicity: 0.3 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5 mM Ammonium Sulphate, 0.4 M Sodium Chloride, 0.1 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2017 / Details: Compound Refractive Lens | |||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.2→19.72 Å / Num. obs: 37901 / % possible obs: 97.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.02 / Rrim(I) all: 0.041 / Net I/σ(I): 15.5 / Num. measured all: 146195 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.6 %
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4E3U Resolution: 1.2→19.719 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 17.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.76 Å2 / Biso mean: 17.5061 Å2 / Biso min: 9.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→19.719 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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